A Poisson-Boltzmann Equation Test Model for Protein in Spherical Solute Region and its Applications

• Autorzy: Yi Jiang , Jinyong Ying , Dexuan Xie
• Języki publikacji: EN

Abstrakty

EN

The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. Several numerical algorithms and program packages have been developed but verification and comparison between them remains an interesting topic. In this paper, a PBE test model is presented for a protein in a spherical solute region, along with its analytical solution. It is then used to verify a PBE finite element solver and applied to a numerical comparison study between a finite element solver and a finite difference solver. Such a study demonstrates the importance of retaining the interface conditions in the development of PBE solvers.

Słowa kluczowe

EN

Poisson-Boltzmann equation; continuum electrostatics; finite element method; finite difference method; electrostatic potential

• Wydawca: De Gruyter Open
• Czasopismo: Molecular Based Mathematical Biology
• Rocznik: 2014
• Tom: 2
• Numer: 1

Daty

otrzymano

2014-04-13

zaakceptowano

2014-08-16

online

2014-09-27

Twórcy

autor

Yi Jiang

• Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201-0413, USA

autor

Jinyong Ying

• Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201-0413, USA

autor

Dexuan Xie

• Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201-0413, USA,

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Identyfikatory

DOI

10.2478/mlbmb-2014-0006